No, 64-bit Intel CPUs run the same instruction set, though there are differences in implementation of PAE NX on some Intel processors -- see the opening paragraph of www.openbsd.org/amd64.html for details.

For help with diagnosing your problem, please post your dmesg and a sample of the incorrect top output.

The load values looks reasonable, but there were no active/running processes other than top. If it happens again, just run a looping shell script, or something else that should busy out one or both CPUs, such as sysutils/stress.

not quite sure about this, but my understanding is that this is caused by TOP sampling interval. Top get CPU utilization statistics every second, but on a idle server, most processes finish their operation within, say, 200 mili seconds, so Top just reports 0 utilization.